Metal Ion Binding in Biological Systems

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Questions and Answers

What is the primary role of metal ions in some metalloproteins?

  • To organize the structures of biomolecules
  • To facilitate a variety of chemical reactions
  • To catalyze the condensation of aspartate and N-carbamoyl phosphate
  • To play a purely structural role (correct)

What happens to the coordinated water molecules when metal ions bind to protein sites?

  • They remain attached to the metal ion
  • They are replaced by nucleotides
  • They are discarded (correct)
  • They are shared with other metal ions

What is the significance of the large ionic radii of metal ions?

  • They can afford high coordination numbers (correct)
  • They can stabilize protein structures
  • They can facilitate a variety of chemical reactions
  • They can catalyze the condensation of aspartate and N-carbamoyl phosphate

What is the importance of the formation of cross-links in some inorganic-element-based drugs?

<p>It is crucial for the mechanism of action of the drugs (B)</p> Signup and view all the answers

What is the role of the metal center in the enzyme aspartate transcarbamoylase (ATCase)?

<p>To stabilize the structure of the enzyme (A)</p> Signup and view all the answers

What is the result of the reaction catalyzed by aspartate transcarbamoylase (ATCase)?

<p>The formation of carbamoyl aspartate plus inorganic phosphate (D)</p> Signup and view all the answers

What is the effect of adding CTP to the enzyme aspartate transcarbamoylase?

<p>It decreases enzyme activity (C)</p> Signup and view all the answers

What is the function of the regulatory subunit in the holoenzyme?

<p>It contains binding sites for inhibitors and activators (D)</p> Signup and view all the answers

What is the result of partial disruption of the quaternary structure of the enzyme?

<p>The catalytic and regulatory units separate (C)</p> Signup and view all the answers

What is the role of the zinc ions in the holoenzyme?

<p>They stabilize domains involved in interactions between the regulatory and catalytic subunits (A)</p> Signup and view all the answers

What is the effect of an inhibitor on the enzyme's quaternary structure?

<p>It shifts the equilibrium towards the T state (C)</p> Signup and view all the answers

What is the structure of the native enzyme aspartate transcarbamoylase?

<p>It has a D, symmetry (A)</p> Signup and view all the answers

What is the result of modifying approximately 24 cysteine residues in the enzyme?

<p>The six zinc ions are released from the holoenzyme (C)</p> Signup and view all the answers

What is the function of the catalytic subunit in the holoenzyme?

<p>It contains the active site for the enzyme (D)</p> Signup and view all the answers

What is the effect of adding ATP to the enzyme aspartate transcarbamoylase?

<p>It increases enzyme activity (D)</p> Signup and view all the answers

What is the model that explains the allosteric behavior of ATCase?

<p>The Monod-Wyman-Changeux model (C)</p> Signup and view all the answers

What was the outcome of cleaving the cysteinate-mercury adducts with excess thiol?

<p>Formation of apo-regulatory subunits that reassociate with the catalytic subunit only when zinc is added (C)</p> Signup and view all the answers

What is the consequence of adding the zinc domain to the catalytic domains?

<p>The affinity for aspartate becomes about twice that of the isolated catalytic domains (A)</p> Signup and view all the answers

What is the role of zinc in transcription factor IIIA (TFIIIA)?

<p>Zinc is essential for specific binding to DNA (C)</p> Signup and view all the answers

What is the characteristic feature of the nine tandem sequences in TFIIIA?

<p>They have a repetitive sequence of cysteines and histidines (A)</p> Signup and view all the answers

What is the proposed structure of each of the nine sequences in TFIIIA?

<p>A zinc-binding domain organized around a zinc ion bound to the invariant cysteine and histidine residues (B)</p> Signup and view all the answers

What is the effect of removing zinc from TFIIIA on its DNA-binding activity?

<p>It abolishes DNA-binding activity (D)</p> Signup and view all the answers

What is the role of the zinc domain in the regulatory subunit?

<p>It allows formation of a small protein domain that binds to the catalytic subunit in a manner that produces conversion from a T-like to an R-like state (A)</p> Signup and view all the answers

What is the stoichiometry of the complex formed between the zinc domain and the catalytic trimer?

<p>3:1 (B)</p> Signup and view all the answers

What is the effect of adding zinc to the TFIIIA-5S RNA complex after EDTA treatment?

<p>It restores specific binding activity (C)</p> Signup and view all the answers

What is the number of zinc ions bound to each TFIIIA protein?

<p>7-11 (D)</p> Signup and view all the answers

What is the term given to the domains in the proposed structure?

<p>Zinc fingers (B)</p> Signup and view all the answers

What technique was used to probe the nature of the ligands coordinated to the zinc ions?

<p>EXAFS spectroscopy (C)</p> Signup and view all the answers

What is the distance of the sulfur atoms from the zinc ion in the EXAFS spectra?

<p>2.30 A (B)</p> Signup and view all the answers

What is the ion that binds to the peptide corresponding to the second zinc-finger domain of TFIIIA?

<p>Zn2+ (A)</p> Signup and view all the answers

What is the shape of the coordination in the cobalt complex?

<p>Tetrahedral (B)</p> Signup and view all the answers

What is the effect of adding zinc ions to the peptide on its susceptibility to cleavage by trypsin?

<p>It decreases its susceptibility (C)</p> Signup and view all the answers

What is the relative affinity of Zn2+ compared to other ions?

<p>103-105 times more tightly (C)</p> Signup and view all the answers

What is the estimated number of genes in the human genome that encode zinc-finger domains?

<p>500 (C)</p> Signup and view all the answers

What is the range of domains in a single protein?

<p>1-37 (B)</p> Signup and view all the answers

What is the effect of adding zinc ions to the peptide on its structure?

<p>It induces a well-ordered structure (A)</p> Signup and view all the answers

What is the common feature among the zinc finger proteins shown in Figure 7.4?

<p>The number of zinc finger domains (D)</p> Signup and view all the answers

What is the approximate diameter of each virus particle capsid?

<p>50 nm (B)</p> Signup and view all the answers

What is the role of zinc binding in the protein classes discussed in the text?

<p>To induce structural changes and stabilization (B)</p> Signup and view all the answers

What is the coordination of zinc in a zinc finger domain?

<p>Two cysteinate and two histidine residues (C)</p> Signup and view all the answers

What is the potential role of zinc in gene-regulatory networks?

<p>Both as a structural device and an information carrier or messenger (D)</p> Signup and view all the answers

What is the consequence of the structure of a zinc finger domain?

<p>The amino and carboxyl termini are far from each other (B)</p> Signup and view all the answers

What is the function of calmodulin in signal transduction pathways?

<p>To sense changes in intracellular calcium concentrations (A)</p> Signup and view all the answers

What is the organization of the cysteines in the steroid receptor superfamily?

<p>Two units of four cysteine residues each (C)</p> Signup and view all the answers

What is the role of one of the zinc-based units in the steroid receptor superfamily?

<p>Dimerization of the protein (D)</p> Signup and view all the answers

How many Ca2+ ions can calmodulin bind?

<p>Four (C)</p> Signup and view all the answers

What was the discovery that led to the identification of zinc in GAL4?

<p>A yeast strain with a mutant GAL4 gene (A)</p> Signup and view all the answers

What is the term for the calcium-binding structure in calmodulin?

<p>EF hand (B)</p> Signup and view all the answers

What is the coordination number of each calcium ion in the EF-hand unit?

<p>Seven (D)</p> Signup and view all the answers

What is the configuration of the proline residue in the GAL4 protein?

<p>Cis peptide bond (B)</p> Signup and view all the answers

What is the function of the retroviral nucleocapsid proteins?

<p>Retroviral replication (D)</p> Signup and view all the answers

What is the nature of the residues that bind to calcium in the EF-hand unit?

<p>Negatively charged (B)</p> Signup and view all the answers

What is the significance of the paired EF-hand domains in calmodulin?

<p>The two members of a pair pack against each other via nonpolar residues (B)</p> Signup and view all the answers

What has been demonstrated by EXAFS experiments on retroviral nucleocapsid proteins?

<p>The presence of zinc inside intact retrovirus particles (B)</p> Signup and view all the answers

What has been revealed by NMR studies on zinc finger domains?

<p>The three-dimensional structure of the domains (A)</p> Signup and view all the answers

What is the consequence of zinc binding in nucleic acid-binding proteins?

<p>Induction of structural changes and stabilization (B)</p> Signup and view all the answers

What is the key factor that favors Ca2+ binding over Mg2+ binding in EF-hand sites?

<p>The smaller size of Mg2+ ions (A)</p> Signup and view all the answers

What is the range of dissociation constants for Ca2+ binding to calmodulin?

<p>1 nM to 1 μM (B)</p> Signup and view all the answers

What is the shape of the calmodulin molecule?

<p>Dumbbell-shaped (A)</p> Signup and view all the answers

What type of structures do the regions responsible for calmodulin binding tend to form?

<p>Alpha-helical structures (C)</p> Signup and view all the answers

What is the purpose of the hydrophobic patches on the surface of the calmodulin lobes?

<p>To facilitate binding to target molecules (B)</p> Signup and view all the answers

What is the characteristic feature of the long alpha helix in calmodulin?

<p>It is stabilized by salt bridges (D)</p> Signup and view all the answers

What is the typical dissociation constant for calmodulin binding to its targets?

<p>1 nM to 1 μM (A)</p> Signup and view all the answers

What is the effect of calmodulin binding to its target molecules?

<p>It enhances the activity of the target molecule (C)</p> Signup and view all the answers

What is the role of the E and F helices in the EF-hand domain?

<p>They form the calcium-binding site (B)</p> Signup and view all the answers

What is the significance of the seven calcium-bound oxygen atoms in the EF-hand domain?

<p>They are derived from amino acid side chains and the peptide backbone (A)</p> Signup and view all the answers

What is the role of calcium in cellular processes?

<p>It binds to calmodulin, leading to conformational changes and target activation (A)</p> Signup and view all the answers

What is the function of membrane-permeable fluorescent calcium-binding dyes like Fura-2?

<p>To measure the changes in intracellular calcium concentration (C)</p> Signup and view all the answers

What is the effect of adding phenylephrine to cells from a vascular smooth muscle cell line?

<p>It increases intracellular calcium levels to approximately 0.5 millimolar (C)</p> Signup and view all the answers

What is the role of counterions in nucleic acid structure?

<p>To neutralize the negatively charged phosphate groups (D)</p> Signup and view all the answers

What is the effect of increasing intracellular calcium concentration on calmodulin?

<p>It increases the binding of calcium to calmodulin, leading to conformational changes (D)</p> Signup and view all the answers

What is the significance of the increase in intracellular calcium levels in response to phenylephrine treatment?

<p>It is a signaling event that can activate specific cellular processes (A)</p> Signup and view all the answers

What is the significance of methionine residues in the hydrophobic patches of calmodulin?

<p>They contribute nearly 50 percent of the accessible surface (A)</p> Signup and view all the answers

What is the result of the binding of calcium to calmodulin?

<p>It induces conformational changes in the protein (A)</p> Signup and view all the answers

What is the role of the central helix in calmodulin?

<p>It is unwound to form a bend upon target peptide binding (C)</p> Signup and view all the answers

What is the characteristic feature of the peptides that bind to calmodulin?

<p>They have a specific sequence motif (C)</p> Signup and view all the answers

What is the function of the two lobes of calmodulin?

<p>They interact with target peptides (D)</p> Signup and view all the answers

What is the outcome of the binding of target peptides to calmodulin?

<p>The target peptide is encapsulated (C)</p> Signup and view all the answers

What is the role of the hydrophobic surfaces on the two calcium-binding lobes of calmodulin?

<p>They interact with target peptides (A)</p> Signup and view all the answers

What is the significance of the flexibility of the connecting helix in calmodulin?

<p>It enables the binding of target peptides (D)</p> Signup and view all the answers

What is the outcome of the structural studies of the calmodulin-target peptide complexes?

<p>The complexes have approximate twofold symmetry (A)</p> Signup and view all the answers

What is the significance of the analysis of the calmodulin complex with a 26-residue peptide from skeletal-muscle myosin light-chain kinase?

<p>It demonstrated the use of newly developed NMR methods (C)</p> Signup and view all the answers

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